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sentences

Id Subject Object Predicate Lexical cue
TextSentencer_T1 0-113 Sentence denotes Expression and epigenetic modulation of sonic hedgehog-GLI1 pathway genes in neuroblastoma cell lines and tumors.
TextSentencer_T2 114-223 Sentence denotes It is well known that sonic hedgehog signaling pathway plays a vital role during early embryonic development.
TextSentencer_T3 224-400 Sentence denotes It is also responsible for stem cell renewal and development of several cancers like colorectal and breast carcinoma and major brain tumors as medulloblastoma and glioblastoma.
TextSentencer_T4 401-511 Sentence denotes The role of sonic hedgehog signaling in the development of neuroblastoma has not been thoroughly investigated.
TextSentencer_T5 512-949 Sentence denotes In this study, we attempted to determine the expression of Bmi-1 stem cell marker and of Shh pathway downstream target genes glioma-associated oncogene homolog 1 (GLI1), protein patched homolog 1 (PTCH1), Cyclin D2, plakoglobin (γ catenin), NK2 homeobox 2 (NKX2.2), paired box gene 6 (PAX6), secreted frizzled-related protein 1 (SFRP1), and hedgehog interacting protein (HHIP) in 11 neuroblastoma cell lines and 41 neuroblastoma samples.
TextSentencer_T6 950-1061 Sentence denotes Also, inhibition of the pathway was performed genetically by GLI1 knockdown siRNA or chemically by cyclopamine.
TextSentencer_T7 1062-1176 Sentence denotes After inhibition, low transcript expression was detected in downstream target genes like PTCH1, in the cell lines.
TextSentencer_T8 1177-1366 Sentence denotes We further preformed promoter methylation studies of Cyclin D2, PTCH1, HHIP, and SFRP1 genes by melting curve analysis-based methylation assay (MCA-Meth) and methylation-specific PCR (MSP).
TextSentencer_T9 1367-1680 Sentence denotes Results revealed no methylation in Cyclin D2 gene promoter in neuroblastoma samples or in cell lines; one cell line (MHH-NB-11) showed PTCH1 methylation; 3/11 (27%) cell lines and 9/41 (22%) neuroblastoma samples showed HHIP methylation; and 3/11 (27%) cell lines and 11/41 (27%) samples showed SFRP1 methylation.
TextSentencer_T10 1681-1936 Sentence denotes Taken together, our results suggest the possibility of two levels of control of the sonic hedgehog signaling pathway: transcriptional and epigenetic, which might offer new therapeutic possibilities to modulate the pathway and try to suppress tumor growth.
T1 0-113 Sentence denotes Expression and epigenetic modulation of sonic hedgehog-GLI1 pathway genes in neuroblastoma cell lines and tumors.
T2 114-223 Sentence denotes It is well known that sonic hedgehog signaling pathway plays a vital role during early embryonic development.
T3 224-400 Sentence denotes It is also responsible for stem cell renewal and development of several cancers like colorectal and breast carcinoma and major brain tumors as medulloblastoma and glioblastoma.
T4 401-511 Sentence denotes The role of sonic hedgehog signaling in the development of neuroblastoma has not been thoroughly investigated.
T5 512-949 Sentence denotes In this study, we attempted to determine the expression of Bmi-1 stem cell marker and of Shh pathway downstream target genes glioma-associated oncogene homolog 1 (GLI1), protein patched homolog 1 (PTCH1), Cyclin D2, plakoglobin (γ catenin), NK2 homeobox 2 (NKX2.2), paired box gene 6 (PAX6), secreted frizzled-related protein 1 (SFRP1), and hedgehog interacting protein (HHIP) in 11 neuroblastoma cell lines and 41 neuroblastoma samples.
T6 950-1061 Sentence denotes Also, inhibition of the pathway was performed genetically by GLI1 knockdown siRNA or chemically by cyclopamine.
T7 1062-1176 Sentence denotes After inhibition, low transcript expression was detected in downstream target genes like PTCH1, in the cell lines.
T8 1177-1366 Sentence denotes We further preformed promoter methylation studies of Cyclin D2, PTCH1, HHIP, and SFRP1 genes by melting curve analysis-based methylation assay (MCA-Meth) and methylation-specific PCR (MSP).
T9 1367-1680 Sentence denotes Results revealed no methylation in Cyclin D2 gene promoter in neuroblastoma samples or in cell lines; one cell line (MHH-NB-11) showed PTCH1 methylation; 3/11 (27%) cell lines and 9/41 (22%) neuroblastoma samples showed HHIP methylation; and 3/11 (27%) cell lines and 11/41 (27%) samples showed SFRP1 methylation.
T10 1681-1936 Sentence denotes Taken together, our results suggest the possibility of two levels of control of the sonic hedgehog signaling pathway: transcriptional and epigenetic, which might offer new therapeutic possibilities to modulate the pathway and try to suppress tumor growth.

DisGeNET

Id Subject Object Predicate Lexical cue
T0 1402-1411 gene:894 denotes Cyclin D2
T1 1429-1442 disease:C0027819 denotes neuroblastoma
T2 1402-1411 gene:894 denotes Cyclin D2
T3 1429-1442 disease:C0700095 denotes neuroblastoma
T4 1402-1411 gene:894 denotes Cyclin D2
T5 1558-1571 disease:C0027819 denotes neuroblastoma
T6 1402-1411 gene:894 denotes Cyclin D2
T7 1558-1571 disease:C0700095 denotes neuroblastoma
T8 1587-1591 gene:64399 denotes HHIP
T9 1429-1442 disease:C0027819 denotes neuroblastoma
T10 1587-1591 gene:64399 denotes HHIP
T11 1429-1442 disease:C0700095 denotes neuroblastoma
T12 1587-1591 gene:64399 denotes HHIP
T13 1558-1571 disease:C0027819 denotes neuroblastoma
T14 1587-1591 gene:64399 denotes HHIP
T15 1558-1571 disease:C0700095 denotes neuroblastoma
T16 1662-1667 gene:6422 denotes SFRP1
T17 1429-1442 disease:C0027819 denotes neuroblastoma
T18 1662-1667 gene:6422 denotes SFRP1
T19 1429-1442 disease:C0700095 denotes neuroblastoma
T20 1662-1667 gene:6422 denotes SFRP1
T21 1558-1571 disease:C0027819 denotes neuroblastoma
T22 1662-1667 gene:6422 denotes SFRP1
T23 1558-1571 disease:C0700095 denotes neuroblastoma
R1 T0 T1 associated_with Cyclin D2,neuroblastoma
R2 T2 T3 associated_with Cyclin D2,neuroblastoma
R3 T4 T5 associated_with Cyclin D2,neuroblastoma
R4 T6 T7 associated_with Cyclin D2,neuroblastoma
R5 T8 T9 associated_with HHIP,neuroblastoma
R6 T10 T11 associated_with HHIP,neuroblastoma
R7 T12 T13 associated_with HHIP,neuroblastoma
R8 T14 T15 associated_with HHIP,neuroblastoma
R9 T16 T17 associated_with SFRP1,neuroblastoma
R10 T18 T19 associated_with SFRP1,neuroblastoma
R11 T20 T21 associated_with SFRP1,neuroblastoma
R12 T22 T23 associated_with SFRP1,neuroblastoma

PubmedHPO

Id Subject Object Predicate Lexical cue
T1 296-303 HP_0002664 denotes cancers
T2 324-340 HP_0003002 denotes breast carcinoma
T3 357-363 HP_0002664 denotes tumors
T4 367-382 HP_0002885 denotes medulloblastoma
T5 387-399 HP_0100843 denotes glioblastoma
T6 460-473 HP_0003006 denotes neuroblastoma
T7 637-643 HP_0009733 denotes glioma
T8 895-908 HP_0003006 denotes neuroblastoma
T9 927-940 HP_0003006 denotes neuroblastoma
T10 1429-1442 HP_0003006 denotes neuroblastoma
T11 1558-1571 HP_0003006 denotes neuroblastoma
T12 1923-1928 HP_0002664 denotes tumor

Allie

Id Subject Object Predicate Lexical cue
SS1_20830616_4_0 637-673 expanded denotes glioma-associated oncogene homolog 1
SS2_20830616_4_0 675-679 abbr denotes GLI1
SS1_20830616_4_1 690-707 expanded denotes patched homolog 1
SS2_20830616_4_1 709-714 abbr denotes PTCH1
SS1_20830616_4_2 753-767 expanded denotes NK2 homeobox 2
SS2_20830616_4_2 769-775 abbr denotes NKX2.2
SS1_20830616_4_3 778-795 expanded denotes paired box gene 6
SS2_20830616_4_3 797-801 abbr denotes PAX6
SS1_20830616_4_4 804-839 expanded denotes secreted frizzled-related protein 1
SS2_20830616_4_4 841-846 abbr denotes SFRP1
SS1_20830616_4_5 853-881 expanded denotes hedgehog interacting protein
SS2_20830616_4_5 883-887 abbr denotes HHIP
SS1_20830616_7_0 1273-1319 expanded denotes melting curve analysis-based methylation assay
SS2_20830616_7_0 1321-1329 abbr denotes MCA-Meth
SS1_20830616_7_1 1335-1359 expanded denotes methylation-specific PCR
SS2_20830616_7_1 1361-1364 abbr denotes MSP
AE1_20830616_4_0 SS1_20830616_4_0 SS2_20830616_4_0 abbreviatedTo glioma-associated oncogene homolog 1,GLI1
AE1_20830616_4_1 SS1_20830616_4_1 SS2_20830616_4_1 abbreviatedTo patched homolog 1,PTCH1
AE1_20830616_4_2 SS1_20830616_4_2 SS2_20830616_4_2 abbreviatedTo NK2 homeobox 2,NKX2.2
AE1_20830616_4_3 SS1_20830616_4_3 SS2_20830616_4_3 abbreviatedTo paired box gene 6,PAX6
AE1_20830616_4_4 SS1_20830616_4_4 SS2_20830616_4_4 abbreviatedTo secreted frizzled-related protein 1,SFRP1
AE1_20830616_4_5 SS1_20830616_4_5 SS2_20830616_4_5 abbreviatedTo hedgehog interacting protein,HHIP
AE1_20830616_7_0 SS1_20830616_7_0 SS2_20830616_7_0 abbreviatedTo melting curve analysis-based methylation assay,MCA-Meth
AE1_20830616_7_1 SS1_20830616_7_1 SS2_20830616_7_1 abbreviatedTo methylation-specific PCR,MSP

DisGeNET5_gene_disease

Id Subject Object Predicate Lexical cue
20830616-0#40#54#gene6469 40-54 gene6469 denotes sonic hedgehog
20830616-0#55#59#gene2735 55-59 gene2735 denotes GLI1
20830616-0#77#90#diseaseC0027819 77-90 diseaseC0027819 denotes neuroblastoma
20830616-0#77#90#diseaseC0700095 77-90 diseaseC0700095 denotes neuroblastoma
20830616-0#77#90#diseaseC0027819 77-90 diseaseC0027819 denotes neuroblastoma
20830616-0#77#90#diseaseC0700095 77-90 diseaseC0700095 denotes neuroblastoma
20830616-4#241#255#gene4821 753-767 gene4821 denotes NK2 homeobox 2
20830616-4#383#396#diseaseC0027819 895-908 diseaseC0027819 denotes neuroblastoma
20830616-4#383#396#diseaseC0700095 895-908 diseaseC0700095 denotes neuroblastoma
20830616-8#35#44#gene894 1402-1411 gene894 denotes Cyclin D2
20830616-8#220#224#gene64399 1587-1591 gene64399 denotes HHIP
20830616-8#295#300#gene6422 1662-1667 gene6422 denotes SFRP1
20830616-8#62#75#diseaseC0027819 1429-1442 diseaseC0027819 denotes neuroblastoma
20830616-8#62#75#diseaseC0700095 1429-1442 diseaseC0700095 denotes neuroblastoma
20830616-8#191#204#diseaseC0027819 1558-1571 diseaseC0027819 denotes neuroblastoma
20830616-8#191#204#diseaseC0700095 1558-1571 diseaseC0700095 denotes neuroblastoma
20830616-8#62#75#diseaseC0027819 1429-1442 diseaseC0027819 denotes neuroblastoma
20830616-8#62#75#diseaseC0700095 1429-1442 diseaseC0700095 denotes neuroblastoma
20830616-8#191#204#diseaseC0027819 1558-1571 diseaseC0027819 denotes neuroblastoma
20830616-8#191#204#diseaseC0700095 1558-1571 diseaseC0700095 denotes neuroblastoma
20830616-8#62#75#diseaseC0027819 1429-1442 diseaseC0027819 denotes neuroblastoma
20830616-8#62#75#diseaseC0700095 1429-1442 diseaseC0700095 denotes neuroblastoma
20830616-8#191#204#diseaseC0027819 1558-1571 diseaseC0027819 denotes neuroblastoma
20830616-8#191#204#diseaseC0700095 1558-1571 diseaseC0700095 denotes neuroblastoma
40#54#gene646977#90#diseaseC0027819 20830616-0#40#54#gene6469 20830616-0#77#90#diseaseC0027819 associated_with sonic hedgehog,neuroblastoma
40#54#gene646977#90#diseaseC0700095 20830616-0#40#54#gene6469 20830616-0#77#90#diseaseC0700095 associated_with sonic hedgehog,neuroblastoma
40#54#gene646977#90#diseaseC0027819 20830616-0#40#54#gene6469 20830616-0#77#90#diseaseC0027819 associated_with sonic hedgehog,neuroblastoma
40#54#gene646977#90#diseaseC0700095 20830616-0#40#54#gene6469 20830616-0#77#90#diseaseC0700095 associated_with sonic hedgehog,neuroblastoma
55#59#gene273577#90#diseaseC0027819 20830616-0#55#59#gene2735 20830616-0#77#90#diseaseC0027819 associated_with GLI1,neuroblastoma
55#59#gene273577#90#diseaseC0700095 20830616-0#55#59#gene2735 20830616-0#77#90#diseaseC0700095 associated_with GLI1,neuroblastoma
55#59#gene273577#90#diseaseC0027819 20830616-0#55#59#gene2735 20830616-0#77#90#diseaseC0027819 associated_with GLI1,neuroblastoma
55#59#gene273577#90#diseaseC0700095 20830616-0#55#59#gene2735 20830616-0#77#90#diseaseC0700095 associated_with GLI1,neuroblastoma
241#255#gene4821383#396#diseaseC0027819 20830616-4#241#255#gene4821 20830616-4#383#396#diseaseC0027819 associated_with NK2 homeobox 2,neuroblastoma
241#255#gene4821383#396#diseaseC0700095 20830616-4#241#255#gene4821 20830616-4#383#396#diseaseC0700095 associated_with NK2 homeobox 2,neuroblastoma
35#44#gene89462#75#diseaseC0027819 20830616-8#35#44#gene894 20830616-8#62#75#diseaseC0027819 associated_with Cyclin D2,neuroblastoma
35#44#gene89462#75#diseaseC0700095 20830616-8#35#44#gene894 20830616-8#62#75#diseaseC0700095 associated_with Cyclin D2,neuroblastoma
35#44#gene894191#204#diseaseC0027819 20830616-8#35#44#gene894 20830616-8#191#204#diseaseC0027819 associated_with Cyclin D2,neuroblastoma
35#44#gene894191#204#diseaseC0700095 20830616-8#35#44#gene894 20830616-8#191#204#diseaseC0700095 associated_with Cyclin D2,neuroblastoma
35#44#gene89462#75#diseaseC0027819 20830616-8#35#44#gene894 20830616-8#62#75#diseaseC0027819 associated_with Cyclin D2,neuroblastoma
35#44#gene89462#75#diseaseC0700095 20830616-8#35#44#gene894 20830616-8#62#75#diseaseC0700095 associated_with Cyclin D2,neuroblastoma
35#44#gene894191#204#diseaseC0027819 20830616-8#35#44#gene894 20830616-8#191#204#diseaseC0027819 associated_with Cyclin D2,neuroblastoma
35#44#gene894191#204#diseaseC0700095 20830616-8#35#44#gene894 20830616-8#191#204#diseaseC0700095 associated_with Cyclin D2,neuroblastoma
35#44#gene89462#75#diseaseC0027819 20830616-8#35#44#gene894 20830616-8#62#75#diseaseC0027819 associated_with Cyclin D2,neuroblastoma
35#44#gene89462#75#diseaseC0700095 20830616-8#35#44#gene894 20830616-8#62#75#diseaseC0700095 associated_with Cyclin D2,neuroblastoma
35#44#gene894191#204#diseaseC0027819 20830616-8#35#44#gene894 20830616-8#191#204#diseaseC0027819 associated_with Cyclin D2,neuroblastoma
35#44#gene894191#204#diseaseC0700095 20830616-8#35#44#gene894 20830616-8#191#204#diseaseC0700095 associated_with Cyclin D2,neuroblastoma
220#224#gene6439962#75#diseaseC0027819 20830616-8#220#224#gene64399 20830616-8#62#75#diseaseC0027819 associated_with HHIP,neuroblastoma
220#224#gene6439962#75#diseaseC0700095 20830616-8#220#224#gene64399 20830616-8#62#75#diseaseC0700095 associated_with HHIP,neuroblastoma
220#224#gene64399191#204#diseaseC0027819 20830616-8#220#224#gene64399 20830616-8#191#204#diseaseC0027819 associated_with HHIP,neuroblastoma
220#224#gene64399191#204#diseaseC0700095 20830616-8#220#224#gene64399 20830616-8#191#204#diseaseC0700095 associated_with HHIP,neuroblastoma
220#224#gene6439962#75#diseaseC0027819 20830616-8#220#224#gene64399 20830616-8#62#75#diseaseC0027819 associated_with HHIP,neuroblastoma
220#224#gene6439962#75#diseaseC0700095 20830616-8#220#224#gene64399 20830616-8#62#75#diseaseC0700095 associated_with HHIP,neuroblastoma
220#224#gene64399191#204#diseaseC0027819 20830616-8#220#224#gene64399 20830616-8#191#204#diseaseC0027819 associated_with HHIP,neuroblastoma
220#224#gene64399191#204#diseaseC0700095 20830616-8#220#224#gene64399 20830616-8#191#204#diseaseC0700095 associated_with HHIP,neuroblastoma
220#224#gene6439962#75#diseaseC0027819 20830616-8#220#224#gene64399 20830616-8#62#75#diseaseC0027819 associated_with HHIP,neuroblastoma
220#224#gene6439962#75#diseaseC0700095 20830616-8#220#224#gene64399 20830616-8#62#75#diseaseC0700095 associated_with HHIP,neuroblastoma
220#224#gene64399191#204#diseaseC0027819 20830616-8#220#224#gene64399 20830616-8#191#204#diseaseC0027819 associated_with HHIP,neuroblastoma
220#224#gene64399191#204#diseaseC0700095 20830616-8#220#224#gene64399 20830616-8#191#204#diseaseC0700095 associated_with HHIP,neuroblastoma
295#300#gene642262#75#diseaseC0027819 20830616-8#295#300#gene6422 20830616-8#62#75#diseaseC0027819 associated_with SFRP1,neuroblastoma
295#300#gene642262#75#diseaseC0700095 20830616-8#295#300#gene6422 20830616-8#62#75#diseaseC0700095 associated_with SFRP1,neuroblastoma
295#300#gene6422191#204#diseaseC0027819 20830616-8#295#300#gene6422 20830616-8#191#204#diseaseC0027819 associated_with SFRP1,neuroblastoma
295#300#gene6422191#204#diseaseC0700095 20830616-8#295#300#gene6422 20830616-8#191#204#diseaseC0700095 associated_with SFRP1,neuroblastoma
295#300#gene642262#75#diseaseC0027819 20830616-8#295#300#gene6422 20830616-8#62#75#diseaseC0027819 associated_with SFRP1,neuroblastoma
295#300#gene642262#75#diseaseC0700095 20830616-8#295#300#gene6422 20830616-8#62#75#diseaseC0700095 associated_with SFRP1,neuroblastoma
295#300#gene6422191#204#diseaseC0027819 20830616-8#295#300#gene6422 20830616-8#191#204#diseaseC0027819 associated_with SFRP1,neuroblastoma
295#300#gene6422191#204#diseaseC0700095 20830616-8#295#300#gene6422 20830616-8#191#204#diseaseC0700095 associated_with SFRP1,neuroblastoma
295#300#gene642262#75#diseaseC0027819 20830616-8#295#300#gene6422 20830616-8#62#75#diseaseC0027819 associated_with SFRP1,neuroblastoma
295#300#gene642262#75#diseaseC0700095 20830616-8#295#300#gene6422 20830616-8#62#75#diseaseC0700095 associated_with SFRP1,neuroblastoma
295#300#gene6422191#204#diseaseC0027819 20830616-8#295#300#gene6422 20830616-8#191#204#diseaseC0027819 associated_with SFRP1,neuroblastoma
295#300#gene6422191#204#diseaseC0700095 20830616-8#295#300#gene6422 20830616-8#191#204#diseaseC0700095 associated_with SFRP1,neuroblastoma

DisGeNet-2017-sample

Id Subject Object Predicate Lexical cue
T2237 40-54 gene:6469 denotes sonic hedgehog
T2238 77-90 disease:C0027819 denotes neuroblastoma
T2239 55-59 gene:2735 denotes GLI1
T2240 753-767 gene:4821 denotes NK2 homeobox 2
T2241 895-908 disease:C0027819 denotes neuroblastoma
R1 T2237 T2238 associated_with sonic hedgehog,neuroblastoma
R2 T2237 T2238 associated_with sonic hedgehog,neuroblastoma
R3 T2239 T2238 associated_with GLI1,neuroblastoma
R4 T2239 T2238 associated_with GLI1,neuroblastoma
R5 T2240 T2241 associated_with NK2 homeobox 2,neuroblastoma
R6 T2240 T2241 associated_with NK2 homeobox 2,neuroblastoma

UBERON-AE

Id Subject Object Predicate Lexical cue
PD-UBERON-AE-B_T1 195-210 http://purl.obolibrary.org/obo/UBERON_0019248 denotes early embryonic
PD-UBERON-AE-B_T2 324-330 http://purl.obolibrary.org/obo/UBERON_0000310 denotes breast
PD-UBERON-AE-B_T3 351-356 http://purl.obolibrary.org/obo/UBERON_0000955 denotes brain

performance-test

Id Subject Object Predicate Lexical cue
PD-UBERON-AE-B_T1 324-330 http://purl.obolibrary.org/obo/UBERON_0000310 denotes breast
PD-UBERON-AE-B_T2 351-356 http://purl.obolibrary.org/obo/UBERON_0000955 denotes brain
PD-UBERON-AE-B_T3 195-210 http://purl.obolibrary.org/obo/UBERON_0019248 denotes early embryonic